Research workbench
CD1C in complex with mpm (mannosyl-BETA1-phosphomycoketide)
Analyse CD1C in complex with mpm (mannosyl-BETA1-phosphomycoketide) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OV6
- Type
- protein
- Length
- 376 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin, T-cell surface glycoprotein CD1C, T- cell surface glycoprotein CD1B
- UniProt
- P61769, P29017, P29016
- Ligands
- D12, MK0, NAG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-2-microglobulin, T-cell surface glycoprotein CD1C, T- cell surface glycoprotein CD1B | protein | 376 | 19% helix, 44% strand | P61769, P29017, P29016 |
Ligands and binding sites
- D12 · Dodecane · ligand · chains A
- MK0 · 1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.82 | 0.84 | 74 | D12, MK0 |
| 2 | 542 | 0.69 | 0.78 | 57 | empty |
| 3 | 94 | 0.38 | 0.76 | 20 | empty |
| 4 | 74 | 0.36 | 0.77 | 17 | empty |
| 5 | 58 | 0.26 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3OV6 · CD1c in complex with MPM (mannosyl-beta1-phosphomycoketide) · the same entry in another collection · chain A against A, TM-score 1.00
- P29017 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1C (P29017) · a predicted model of the same protein · chain A against A, TM-score 0.69
- P29016 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1B (P29016) · a predicted model of the same protein · chain A against A, TM-score 0.69
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain A against A, TM-score 0.26
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P61769
- Every structure of UniProt P29017
- Every structure of UniProt P29016
- Elsewhere: RCSB PDB 3OV6 · PDBe 3OV6 · UniProt P61769 · UniProt P29017 · UniProt P29016
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